Starting phenix.real_space_refine (version: dev) on Thu Dec 15 04:29:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/12_2022/7ngl_12315_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/12_2022/7ngl_12315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/12_2022/7ngl_12315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/12_2022/7ngl_12315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/12_2022/7ngl_12315_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/12_2022/7ngl_12315_trim_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "B ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 706": "OE1" <-> "OE2" Residue "B ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 781": "OE1" <-> "OE2" Residue "C ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 897": "OE1" <-> "OE2" Residue "D ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 441": "OE1" <-> "OE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D GLU 583": "OE1" <-> "OE2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 897": "OE1" <-> "OE2" Residue "E ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 441": "OE1" <-> "OE2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "E GLU 495": "OE1" <-> "OE2" Residue "E GLU 583": "OE1" <-> "OE2" Residue "E GLU 614": "OE1" <-> "OE2" Residue "E ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 897": "OE1" <-> "OE2" Residue "F ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 583": "OE1" <-> "OE2" Residue "F ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 812": "OE1" <-> "OE2" Residue "F ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 937": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 74735 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "B" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "C" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "D" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "E" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "F" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.20, per 1000 atoms: 0.35 Number of scatterers: 74735 At special positions: 0 Unit cell: (143.763, 146.256, 224.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 162 16.00 P 12 15.00 O 6978 8.00 N 6426 7.00 C 23442 6.00 H 37715 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 51.16 Conformation dependent library (CDL) restraints added in 4.9 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 188 helices and 36 sheets defined 43.7% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.832A pdb=" N VAL A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 306 removed outlier: 3.681A pdb=" N GLU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.746A pdb=" N LEU A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 355 through 406 removed outlier: 3.952A pdb=" N LEU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 427 removed outlier: 3.814A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 4.208A pdb=" N ASP A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 495 through 508 Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.695A pdb=" N LEU A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 618 removed outlier: 3.660A pdb=" N ASN A 618 " --> pdb=" O GLN A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 618' Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 663 through 673 removed outlier: 3.998A pdb=" N LEU A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG A 672 " --> pdb=" O ALA A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 681 Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 710 through 728 Processing helix chain 'A' and resid 742 through 746 Processing helix chain 'A' and resid 808 through 828 removed outlier: 4.028A pdb=" N MET A 826 " --> pdb=" O ARG A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 869 Proline residue: A 854 - end of helix removed outlier: 4.397A pdb=" N CYS A 858 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 861 " --> pdb=" O CYS A 858 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A 869 " --> pdb=" O SER A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 919 through 922 Processing helix chain 'A' and resid 925 through 928 No H-bonds generated for 'chain 'A' and resid 925 through 928' Processing helix chain 'A' and resid 939 through 944 Processing helix chain 'B' and resid 149 through 155 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.772A pdb=" N VAL B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.849A pdb=" N GLU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 328 through 338 removed outlier: 4.077A pdb=" N LEU B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 355 through 388 Processing helix chain 'B' and resid 393 through 405 Processing helix chain 'B' and resid 414 through 427 Processing helix chain 'B' and resid 432 through 447 Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 495 through 508 Processing helix chain 'B' and resid 529 through 540 removed outlier: 3.713A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 559 Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.743A pdb=" N LEU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 618 removed outlier: 3.687A pdb=" N ASN B 618 " --> pdb=" O GLN B 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 615 through 618' Processing helix chain 'B' and resid 647 through 650 No H-bonds generated for 'chain 'B' and resid 647 through 650' Processing helix chain 'B' and resid 665 through 673 removed outlier: 4.072A pdb=" N ARG B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 681 Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 710 through 728 Processing helix chain 'B' and resid 739 through 746 removed outlier: 4.252A pdb=" N GLN B 743 " --> pdb=" O PRO B 739 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 828 removed outlier: 3.594A pdb=" N MET B 826 " --> pdb=" O ARG B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 869 Proline residue: B 854 - end of helix removed outlier: 4.219A pdb=" N CYS B 858 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 861 " --> pdb=" O CYS B 858 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET B 869 " --> pdb=" O SER B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 914 through 922 removed outlier: 4.451A pdb=" N LYS B 918 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE B 920 " --> pdb=" O LYS B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 928 No H-bonds generated for 'chain 'B' and resid 925 through 928' Processing helix chain 'B' and resid 939 through 944 Processing helix chain 'C' and resid 149 through 155 Processing helix chain 'C' and resid 175 through 180 removed outlier: 3.741A pdb=" N VAL C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 306 removed outlier: 3.682A pdb=" N GLU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 328 through 338 removed outlier: 3.836A pdb=" N LEU C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 355 through 405 removed outlier: 3.599A pdb=" N LEU C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS C 393 " --> pdb=" O GLN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 427 Processing helix chain 'C' and resid 432 through 447 Processing helix chain 'C' and resid 453 through 466 Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 495 through 510 removed outlier: 3.721A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 540 Processing helix chain 'C' and resid 555 through 559 Processing helix chain 'C' and resid 572 through 580 Processing helix chain 'C' and resid 592 through 594 No H-bonds generated for 'chain 'C' and resid 592 through 594' Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.694A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 removed outlier: 3.738A pdb=" N ASN C 618 " --> pdb=" O GLN C 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 615 through 618' Processing helix chain 'C' and resid 647 through 650 No H-bonds generated for 'chain 'C' and resid 647 through 650' Processing helix chain 'C' and resid 663 through 673 removed outlier: 3.979A pdb=" N LEU C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG C 672 " --> pdb=" O ALA C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 682 Processing helix chain 'C' and resid 693 through 702 Processing helix chain 'C' and resid 710 through 728 Processing helix chain 'C' and resid 739 through 746 removed outlier: 3.967A pdb=" N GLN C 743 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 828 removed outlier: 3.801A pdb=" N MET C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 869 Proline residue: C 854 - end of helix removed outlier: 4.318A pdb=" N CYS C 858 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 861 " --> pdb=" O CYS C 858 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET C 869 " --> pdb=" O SER C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 914 through 916 No H-bonds generated for 'chain 'C' and resid 914 through 916' Processing helix chain 'C' and resid 919 through 922 Processing helix chain 'C' and resid 925 through 928 No H-bonds generated for 'chain 'C' and resid 925 through 928' Processing helix chain 'C' and resid 939 through 944 Processing helix chain 'D' and resid 148 through 155 removed outlier: 3.820A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 291 through 306 removed outlier: 3.554A pdb=" N GLU D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 328 through 338 removed outlier: 3.915A pdb=" N LEU D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 355 through 388 Processing helix chain 'D' and resid 392 through 404 Processing helix chain 'D' and resid 414 through 427 Processing helix chain 'D' and resid 432 through 447 Processing helix chain 'D' and resid 453 through 467 Processing helix chain 'D' and resid 480 through 488 Processing helix chain 'D' and resid 495 through 510 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 592 through 594 No H-bonds generated for 'chain 'D' and resid 592 through 594' Processing helix chain 'D' and resid 603 through 611 removed outlier: 4.125A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 650 No H-bonds generated for 'chain 'D' and resid 647 through 650' Processing helix chain 'D' and resid 663 through 673 removed outlier: 3.997A pdb=" N LEU D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG D 672 " --> pdb=" O ALA D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 681 Processing helix chain 'D' and resid 693 through 702 Processing helix chain 'D' and resid 710 through 728 Processing helix chain 'D' and resid 742 through 746 Processing helix chain 'D' and resid 808 through 828 removed outlier: 3.560A pdb=" N MET D 826 " --> pdb=" O ARG D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 869 Proline residue: D 854 - end of helix removed outlier: 4.316A pdb=" N CYS D 858 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 861 " --> pdb=" O CYS D 858 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET D 869 " --> pdb=" O SER D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 914 through 916 No H-bonds generated for 'chain 'D' and resid 914 through 916' Processing helix chain 'D' and resid 919 through 922 Processing helix chain 'D' and resid 925 through 928 No H-bonds generated for 'chain 'D' and resid 925 through 928' Processing helix chain 'D' and resid 939 through 944 Processing helix chain 'E' and resid 148 through 155 removed outlier: 3.661A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 removed outlier: 3.616A pdb=" N VAL E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 306 Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 328 through 338 removed outlier: 4.013A pdb=" N LEU E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 351 Processing helix chain 'E' and resid 355 through 404 removed outlier: 3.867A pdb=" N LEU E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 427 Processing helix chain 'E' and resid 432 through 447 removed outlier: 3.789A pdb=" N GLY E 446 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 466 removed outlier: 3.686A pdb=" N VAL E 457 " --> pdb=" O SER E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 488 Processing helix chain 'E' and resid 495 through 511 removed outlier: 3.753A pdb=" N ARG E 511 " --> pdb=" O VAL E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 540 Processing helix chain 'E' and resid 555 through 558 Processing helix chain 'E' and resid 572 through 580 Processing helix chain 'E' and resid 592 through 594 No H-bonds generated for 'chain 'E' and resid 592 through 594' Processing helix chain 'E' and resid 603 through 611 removed outlier: 3.808A pdb=" N LEU E 608 " --> pdb=" O SER E 604 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 618 Processing helix chain 'E' and resid 647 through 650 No H-bonds generated for 'chain 'E' and resid 647 through 650' Processing helix chain 'E' and resid 663 through 673 removed outlier: 4.252A pdb=" N ARG E 672 " --> pdb=" O ALA E 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 682 Processing helix chain 'E' and resid 693 through 702 Processing helix chain 'E' and resid 710 through 728 Processing helix chain 'E' and resid 742 through 746 Processing helix chain 'E' and resid 808 through 828 removed outlier: 3.891A pdb=" N MET E 826 " --> pdb=" O ARG E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 850 through 869 Proline residue: E 854 - end of helix removed outlier: 4.404A pdb=" N CYS E 858 " --> pdb=" O SER E 855 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 861 " --> pdb=" O CYS E 858 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 865 " --> pdb=" O THR E 862 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET E 869 " --> pdb=" O SER E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 904 Processing helix chain 'E' and resid 914 through 916 No H-bonds generated for 'chain 'E' and resid 914 through 916' Processing helix chain 'E' and resid 919 through 922 Processing helix chain 'E' and resid 925 through 928 No H-bonds generated for 'chain 'E' and resid 925 through 928' Processing helix chain 'E' and resid 939 through 945 Processing helix chain 'F' and resid 150 through 155 Processing helix chain 'F' and resid 175 through 180 removed outlier: 3.807A pdb=" N VAL F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 306 removed outlier: 3.793A pdb=" N GLU F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 328 through 338 removed outlier: 3.935A pdb=" N LEU F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 351 Processing helix chain 'F' and resid 355 through 388 Processing helix chain 'F' and resid 392 through 404 Processing helix chain 'F' and resid 414 through 425 removed outlier: 4.271A pdb=" N LYS F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE F 421 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 removed outlier: 3.844A pdb=" N GLY F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU F 447 " --> pdb=" O SER F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 480 through 488 Processing helix chain 'F' and resid 495 through 508 Processing helix chain 'F' and resid 529 through 540 Processing helix chain 'F' and resid 555 through 559 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 592 through 594 No H-bonds generated for 'chain 'F' and resid 592 through 594' Processing helix chain 'F' and resid 603 through 611 removed outlier: 3.730A pdb=" N LEU F 608 " --> pdb=" O SER F 604 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU F 609 " --> pdb=" O SER F 605 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 618 removed outlier: 3.863A pdb=" N ASN F 618 " --> pdb=" O GLN F 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 615 through 618' Processing helix chain 'F' and resid 647 through 650 No H-bonds generated for 'chain 'F' and resid 647 through 650' Processing helix chain 'F' and resid 663 through 673 removed outlier: 4.072A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG F 672 " --> pdb=" O ALA F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 681 Processing helix chain 'F' and resid 686 through 688 No H-bonds generated for 'chain 'F' and resid 686 through 688' Processing helix chain 'F' and resid 693 through 702 Processing helix chain 'F' and resid 710 through 728 Processing helix chain 'F' and resid 739 through 746 removed outlier: 4.278A pdb=" N GLN F 743 " --> pdb=" O PRO F 739 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 828 removed outlier: 4.083A pdb=" N MET F 826 " --> pdb=" O ARG F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 869 Proline residue: F 854 - end of helix removed outlier: 4.398A pdb=" N CYS F 858 " --> pdb=" O SER F 855 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 861 " --> pdb=" O CYS F 858 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET F 869 " --> pdb=" O SER F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 904 Processing helix chain 'F' and resid 914 through 922 removed outlier: 4.214A pdb=" N LYS F 918 " --> pdb=" O GLU F 915 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE F 920 " --> pdb=" O LYS F 917 " (cutoff:3.500A) Processing helix chain 'F' and resid 925 through 928 No H-bonds generated for 'chain 'F' and resid 925 through 928' Processing helix chain 'F' and resid 939 through 944 Processing sheet with id= A, first strand: chain 'A' and resid 140 through 142 Processing sheet with id= B, first strand: chain 'A' and resid 164 through 166 Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.324A pdb=" N CYS A 637 " --> pdb=" O PHE A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.532A pdb=" N LEU A 586 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE A 547 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 588 " --> pdb=" O PHE A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 689 through 691 removed outlier: 7.061A pdb=" N VAL A 735 " --> pdb=" O LYS A 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 764 through 766 Processing sheet with id= G, first strand: chain 'B' and resid 140 through 142 Processing sheet with id= H, first strand: chain 'B' and resid 188 through 191 Processing sheet with id= I, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.182A pdb=" N CYS B 637 " --> pdb=" O PHE B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 544 through 548 removed outlier: 6.516A pdb=" N LEU B 586 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE B 547 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 588 " --> pdb=" O PHE B 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 764 through 766 Processing sheet with id= L, first strand: chain 'B' and resid 910 through 913 removed outlier: 3.640A pdb=" N LEU B 912 " --> pdb=" O HIS B 934 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 140 through 142 Processing sheet with id= N, first strand: chain 'C' and resid 164 through 167 Processing sheet with id= O, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.233A pdb=" N CYS C 637 " --> pdb=" O PHE C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 544 through 548 removed outlier: 6.457A pdb=" N LEU C 586 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE C 547 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU C 588 " --> pdb=" O PHE C 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 764 through 766 Processing sheet with id= R, first strand: chain 'C' and resid 910 through 913 removed outlier: 3.587A pdb=" N LEU C 912 " --> pdb=" O HIS C 934 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 140 through 142 Processing sheet with id= T, first strand: chain 'D' and resid 163 through 167 Processing sheet with id= U, first strand: chain 'D' and resid 544 through 548 removed outlier: 7.156A pdb=" N LEU D 586 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE D 547 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU D 588 " --> pdb=" O PHE D 547 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE D 636 " --> pdb=" O ILE D 589 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 764 through 766 Processing sheet with id= W, first strand: chain 'D' and resid 910 through 913 Processing sheet with id= X, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= Y, first strand: chain 'E' and resid 164 through 166 Processing sheet with id= Z, first strand: chain 'E' and resid 519 through 522 removed outlier: 6.034A pdb=" N GLU E 654 " --> pdb=" O CYS E 520 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TYR E 522 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE E 656 " --> pdb=" O TYR E 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.454A pdb=" N LEU E 586 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE E 547 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU E 588 " --> pdb=" O PHE E 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.844A pdb=" N VAL E 735 " --> pdb=" O LYS E 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 780 through 784 Processing sheet with id= AD, first strand: chain 'E' and resid 910 through 913 Processing sheet with id= AE, first strand: chain 'F' and resid 140 through 142 Processing sheet with id= AF, first strand: chain 'F' and resid 188 through 191 Processing sheet with id= AG, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.172A pdb=" N CYS F 637 " --> pdb=" O PHE F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.664A pdb=" N LEU F 586 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE F 547 " --> pdb=" O LEU F 586 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU F 588 " --> pdb=" O PHE F 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 689 through 691 removed outlier: 6.938A pdb=" N VAL F 735 " --> pdb=" O LYS F 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 764 through 766 1319 hydrogen bonds defined for protein. 3600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.82 Time building geometry restraints manager: 53.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 37673 1.02 - 1.22: 159 1.22 - 1.42: 14911 1.42 - 1.62: 22333 1.62 - 1.82: 283 Bond restraints: 75359 Sorted by residual: bond pdb=" CG GLU E 665 " pdb=" CD GLU E 665 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.34e+01 bond pdb=" CG GLU A 665 " pdb=" CD GLU A 665 " ideal model delta sigma weight residual 1.516 1.427 0.089 2.50e-02 1.60e+03 1.28e+01 bond pdb=" CG GLU C 665 " pdb=" CD GLU C 665 " ideal model delta sigma weight residual 1.516 1.428 0.088 2.50e-02 1.60e+03 1.25e+01 bond pdb=" CG GLU B 665 " pdb=" CD GLU B 665 " ideal model delta sigma weight residual 1.516 1.433 0.083 2.50e-02 1.60e+03 1.11e+01 bond pdb=" CB ILE D 403 " pdb=" CG2 ILE D 403 " ideal model delta sigma weight residual 1.521 1.629 -0.108 3.30e-02 9.18e+02 1.07e+01 ... (remaining 75354 not shown) Histogram of bond angle deviations from ideal: 94.39 - 102.70: 225 102.70 - 111.00: 80189 111.00 - 119.31: 29232 119.31 - 127.62: 26939 127.62 - 135.93: 386 Bond angle restraints: 136971 Sorted by residual: angle pdb=" N GLY F 601 " pdb=" CA GLY F 601 " pdb=" C GLY F 601 " ideal model delta sigma weight residual 113.18 94.39 18.79 2.37e+00 1.78e-01 6.29e+01 angle pdb=" N GLY D 601 " pdb=" CA GLY D 601 " pdb=" C GLY D 601 " ideal model delta sigma weight residual 113.18 95.96 17.22 2.37e+00 1.78e-01 5.28e+01 angle pdb=" N GLY E 601 " pdb=" CA GLY E 601 " pdb=" C GLY E 601 " ideal model delta sigma weight residual 113.18 97.91 15.27 2.37e+00 1.78e-01 4.15e+01 angle pdb=" N GLY C 601 " pdb=" CA GLY C 601 " pdb=" C GLY C 601 " ideal model delta sigma weight residual 113.18 98.76 14.42 2.37e+00 1.78e-01 3.70e+01 angle pdb=" N GLY B 210 " pdb=" CA GLY B 210 " pdb=" C GLY B 210 " ideal model delta sigma weight residual 113.18 100.17 13.01 2.37e+00 1.78e-01 3.01e+01 ... (remaining 136966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 29192 31.27 - 62.53: 610 62.53 - 93.80: 62 93.80 - 125.07: 1 125.07 - 156.34: 3 Dihedral angle restraints: 29868 sinusoidal: 14628 harmonic: 15240 Sorted by residual: dihedral pdb=" O1B ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PB ADP D1001 " pdb=" PA ADP D1001 " ideal model delta sinusoidal sigma weight residual 300.00 143.66 156.34 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 69.25 -129.25 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 66.43 -126.43 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 29865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4739 0.093 - 0.185: 1015 0.185 - 0.278: 70 0.278 - 0.371: 6 0.371 - 0.463: 2 Chirality restraints: 5832 Sorted by residual: chirality pdb=" CB ILE D 558 " pdb=" CA ILE D 558 " pdb=" CG1 ILE D 558 " pdb=" CG2 ILE D 558 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CG LEU C 462 " pdb=" CB LEU C 462 " pdb=" CD1 LEU C 462 " pdb=" CD2 LEU C 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE B 185 " pdb=" CA ILE B 185 " pdb=" CG1 ILE B 185 " pdb=" CG2 ILE B 185 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 5829 not shown) Planarity restraints: 10980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 491 " -0.038 2.00e-02 2.50e+03 3.41e-02 2.62e+01 pdb=" CG HIS E 491 " 0.085 2.00e-02 2.50e+03 pdb=" ND1 HIS E 491 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS E 491 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS E 491 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS E 491 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 HIS E 491 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 HIS E 491 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS E 491 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 615 " 0.024 2.00e-02 2.50e+03 4.80e-02 2.30e+01 pdb=" C GLN E 615 " -0.083 2.00e-02 2.50e+03 pdb=" O GLN E 615 " 0.031 2.00e-02 2.50e+03 pdb=" N ASN E 616 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 861 " -0.024 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C VAL D 861 " 0.082 2.00e-02 2.50e+03 pdb=" O VAL D 861 " -0.031 2.00e-02 2.50e+03 pdb=" N THR D 862 " -0.028 2.00e-02 2.50e+03 ... (remaining 10977 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 7275 2.23 - 2.82: 162404 2.82 - 3.41: 193316 3.41 - 4.01: 243454 4.01 - 4.60: 382428 Nonbonded interactions: 988877 Sorted by model distance: nonbonded pdb=" O GLU E 543 " pdb=" H LEU E 586 " model vdw 1.636 1.850 nonbonded pdb=" O PHE C 619 " pdb=" H VAL C 628 " model vdw 1.649 1.850 nonbonded pdb=" O ASP B 852 " pdb=" HG SER B 855 " model vdw 1.651 1.850 nonbonded pdb=" O ALA C 556 " pdb=" H GLY C 560 " model vdw 1.652 1.850 nonbonded pdb=" O ALA F 556 " pdb=" H GLY F 560 " model vdw 1.653 1.850 ... (remaining 988872 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'B' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'C' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'D' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = chain 'E' selection = (chain 'F' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 162 5.16 5 C 23442 2.51 5 N 6426 2.21 5 O 6978 1.98 5 H 37715 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.830 Extract box with map and model: 17.210 Check model and map are aligned: 0.830 Convert atoms to be neutral: 0.490 Process input model: 185.130 Find NCS groups from input model: 3.680 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 215.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.134 37644 Z= 0.771 Angle : 1.497 18.792 50856 Z= 0.830 Chirality : 0.072 0.463 5832 Planarity : 0.009 0.055 6528 Dihedral : 13.267 156.335 14466 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.22 % Favored : 90.76 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.12), residues: 4632 helix: -2.07 (0.09), residues: 1874 sheet: -3.71 (0.18), residues: 567 loop : -0.47 (0.15), residues: 2191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 397 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 396 time to evaluate : 4.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 397 average time/residue: 1.0337 time to fit residues: 669.4568 Evaluate side-chains 240 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 4.692 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.7988 time to fit residues: 8.3872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 8.9990 chunk 350 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 187 optimal weight: 0.9980 chunk 362 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 269 optimal weight: 20.0000 chunk 419 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 916 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 37644 Z= 0.200 Angle : 0.663 7.726 50856 Z= 0.342 Chirality : 0.041 0.158 5832 Planarity : 0.004 0.047 6528 Dihedral : 7.051 159.121 5130 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4632 helix: -0.66 (0.11), residues: 1901 sheet: -3.41 (0.18), residues: 577 loop : -0.71 (0.14), residues: 2154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 253 time to evaluate : 4.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 266 average time/residue: 0.8840 time to fit residues: 386.6870 Evaluate side-chains 234 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 221 time to evaluate : 4.596 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.6406 time to fit residues: 21.1508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 349 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 420 optimal weight: 0.9990 chunk 454 optimal weight: 1.9990 chunk 374 optimal weight: 5.9990 chunk 416 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 337 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 HIS B 477 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 37644 Z= 0.240 Angle : 0.598 7.257 50856 Z= 0.305 Chirality : 0.039 0.152 5832 Planarity : 0.004 0.062 6528 Dihedral : 6.570 144.186 5130 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.12), residues: 4632 helix: -0.09 (0.11), residues: 1928 sheet: -3.17 (0.19), residues: 602 loop : -0.88 (0.14), residues: 2102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 231 time to evaluate : 4.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 239 average time/residue: 0.9317 time to fit residues: 362.1536 Evaluate side-chains 218 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 4.626 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.6436 time to fit residues: 19.0880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 10.0000 chunk 316 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 282 optimal weight: 20.0000 chunk 421 optimal weight: 0.9980 chunk 446 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 399 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 ASN B 741 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 37644 Z= 0.226 Angle : 0.564 6.960 50856 Z= 0.284 Chirality : 0.039 0.144 5832 Planarity : 0.003 0.039 6528 Dihedral : 6.329 136.515 5130 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.12), residues: 4632 helix: 0.15 (0.12), residues: 1940 sheet: -3.00 (0.20), residues: 578 loop : -1.05 (0.13), residues: 2114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 221 time to evaluate : 5.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 235 average time/residue: 0.9187 time to fit residues: 357.4620 Evaluate side-chains 220 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 4.552 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.7101 time to fit residues: 23.8347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 0.9980 chunk 253 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 332 optimal weight: 20.0000 chunk 184 optimal weight: 7.9990 chunk 381 optimal weight: 4.9990 chunk 308 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 228 optimal weight: 2.9990 chunk 400 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 37644 Z= 0.231 Angle : 0.557 6.779 50856 Z= 0.279 Chirality : 0.039 0.147 5832 Planarity : 0.003 0.040 6528 Dihedral : 6.154 125.962 5130 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.12), residues: 4632 helix: 0.31 (0.12), residues: 1945 sheet: -2.88 (0.21), residues: 578 loop : -1.08 (0.13), residues: 2109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 218 time to evaluate : 4.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 228 average time/residue: 0.9141 time to fit residues: 347.1535 Evaluate side-chains 218 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 208 time to evaluate : 4.670 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6596 time to fit residues: 18.5309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 2.9990 chunk 402 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 262 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 447 optimal weight: 4.9990 chunk 371 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 876 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 37644 Z= 0.175 Angle : 0.531 6.831 50856 Z= 0.263 Chirality : 0.038 0.147 5832 Planarity : 0.003 0.062 6528 Dihedral : 6.015 118.717 5130 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.12), residues: 4632 helix: 0.46 (0.12), residues: 1947 sheet: -2.80 (0.21), residues: 578 loop : -1.05 (0.13), residues: 2107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 215 time to evaluate : 4.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 222 average time/residue: 0.9187 time to fit residues: 340.5015 Evaluate side-chains 209 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 205 time to evaluate : 4.664 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6331 time to fit residues: 10.9184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 254 optimal weight: 20.0000 chunk 326 optimal weight: 8.9990 chunk 252 optimal weight: 20.0000 chunk 376 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 445 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 HIS ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 37644 Z= 0.323 Angle : 0.592 7.127 50856 Z= 0.300 Chirality : 0.040 0.165 5832 Planarity : 0.004 0.055 6528 Dihedral : 6.121 117.639 5130 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.12), residues: 4632 helix: 0.29 (0.12), residues: 1966 sheet: -2.77 (0.21), residues: 583 loop : -1.22 (0.13), residues: 2083 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 210 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 214 average time/residue: 0.9051 time to fit residues: 324.4243 Evaluate side-chains 211 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 204 time to evaluate : 4.592 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6567 time to fit residues: 14.4232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 0.7980 chunk 177 optimal weight: 0.4980 chunk 265 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 283 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 41 optimal weight: 0.0770 chunk 350 optimal weight: 10.0000 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 37644 Z= 0.170 Angle : 0.535 9.928 50856 Z= 0.264 Chirality : 0.038 0.149 5832 Planarity : 0.003 0.057 6528 Dihedral : 5.950 115.428 5130 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.12), residues: 4632 helix: 0.55 (0.12), residues: 1959 sheet: -2.68 (0.21), residues: 572 loop : -1.12 (0.13), residues: 2101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 209 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 214 average time/residue: 0.9631 time to fit residues: 345.3429 Evaluate side-chains 207 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 4.680 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.7243 time to fit residues: 10.1310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 20.0000 chunk 426 optimal weight: 3.9990 chunk 389 optimal weight: 8.9990 chunk 414 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 374 optimal weight: 7.9990 chunk 392 optimal weight: 6.9990 chunk 413 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 37644 Z= 0.325 Angle : 0.585 6.920 50856 Z= 0.295 Chirality : 0.040 0.158 5832 Planarity : 0.004 0.049 6528 Dihedral : 6.052 114.017 5130 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.12), residues: 4632 helix: 0.41 (0.12), residues: 1959 sheet: -2.69 (0.20), residues: 581 loop : -1.24 (0.13), residues: 2092 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 202 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 207 average time/residue: 0.8900 time to fit residues: 306.0170 Evaluate side-chains 206 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 200 time to evaluate : 4.550 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.6598 time to fit residues: 13.1531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 1.9990 chunk 438 optimal weight: 2.9990 chunk 267 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 305 optimal weight: 9.9990 chunk 460 optimal weight: 2.9990 chunk 423 optimal weight: 7.9990 chunk 366 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 283 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 37644 Z= 0.226 Angle : 0.551 8.235 50856 Z= 0.275 Chirality : 0.039 0.147 5832 Planarity : 0.003 0.048 6528 Dihedral : 5.967 112.688 5130 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.12), residues: 4632 helix: 0.53 (0.12), residues: 1958 sheet: -2.67 (0.21), residues: 563 loop : -1.20 (0.13), residues: 2111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 202 time to evaluate : 4.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 205 average time/residue: 0.9261 time to fit residues: 316.4843 Evaluate side-chains 204 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 199 time to evaluate : 4.657 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.7076 time to fit residues: 13.8805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 20.0000 chunk 390 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 337 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 367 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 376 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 460 ASN D 839 HIS ** F 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.161743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3786 r_free = 0.3786 target = 0.116036 restraints weight = 272906.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.113706 restraints weight = 173562.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.113905 restraints weight = 135024.149| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 37644 Z= 0.133 Angle : 0.515 6.899 50856 Z= 0.251 Chirality : 0.038 0.149 5832 Planarity : 0.003 0.053 6528 Dihedral : 5.681 110.397 5130 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4632 helix: 0.81 (0.12), residues: 1947 sheet: -2.49 (0.21), residues: 554 loop : -1.06 (0.13), residues: 2131 =============================================================================== Job complete usr+sys time: 9206.07 seconds wall clock time: 162 minutes 13.04 seconds (9733.04 seconds total)